photosmynthesis's Blog

Rhizosphere tangents
October 29, 2010, 4:20 pm
Filed under: Uncategorized

No matter how educated I become, I seem to still be left in the dirt….squandering about with no hope of escape.  In  a way it makes sense, for this is where some of the most interesting things happen.  There are a wide variety of organisms that occupy the subterranean landscape, and for all there laborious efforts, they go unnoticed by most of us.

Children can learn about the world under them, in addition to around them, by being able to examine directly at the plant rhizosphere. Plant root systems create there own soil communities.  The dynamic of nature of world which exist just below our feet. This is why one possible invention which would help foster curiosity in  children could integrate a Rhizotron.  This tool which allows scientists to measure below ground dynamics of plants could provide a window to the ecological basement of many habitats, increasing the public understanding of the extent of the interconnectedness of natural systems.


Mushroom man
October 29, 2010, 3:03 pm
Filed under: Uncategorized

I know people have heard me rave enough about fungus in our discussions, but I just wanted to do a little more, and also maybe show people why I think they are so awesome.  I spoke before about Paul Stamets, who is amazing to read as well as to watch give talks.  Stamets presents multiple arguments for the utilization of fungus, from anti-cancer and HIV medications, to petroleum clean up and mycofiltration.  Anyway, check it out if you are interested…..


Final Project, Part 1
October 22, 2010, 5:01 am
Filed under: Uncategorized

Callistemon trees, also known as Bottlebrushes, are a wonderful design for cleaning tools.  From washing glassware in the lab, these stiff bristles also have an attractive color scheme and could be used as a temple for how function and appearance.


Whale baleen is strong and fine, and made of keratin.  They create a perfect method for scrubbing and sweeping.  They are also quite flexible, able to bend and flex, which would make them an ideal model for brushes of brooms.


Leaf cutter ants harvest leaves from the canopy trees and carry them extreme distances back to there domains.  The foliage is used to feed a garden of fungus, which is managed by a class of ants of a different size than the outside workers.  These ants must work under sterile conditions.  The process by which they clean them selves could provide us with the ideas about possible natural sterility techniques


Giant tubeworms are very efficient at exchange of gasses and nutrients with there feathery like extensions from of the passing water.  These plumes may be the template for development of air purification systems, which could remove dust and other contaminants from homes of offices


Penicillin was first discovered from bread mold.  Since then there have been more compounds isolated from fungi that could have potential antimicrobial effects.  The very nature of the work that saprophobes perform puts them in contact with many potentially lethal bacteria.  It is not hard to see why this is where we should be looking for our disinfectants.


Plant trichomes perform diverse function in plant, for defense, fruit production as well as for gas exchange.  But the fine scale of these hairs could be used to create delicate take wipers, like the Kimwipes we often use in the lab.


Bacteria using inosital phosphate can reclaim uranium from mine drainage.  Engineering production and utilization of these microbes to clean contaminated areas, could significantly reduce our environmental impact as we increase our investments in nuclear energy.


Hair is a very efficient material in its absorbency.  Booms stuffed with hair have already been implemented to absorb oil from the BP Horizon oil spill.  This could be diversified to more applications, such as household spill clean up.


Hyphal strands of fungi are small in diameter and are able to explore small spaces.  With their additional absorptive capacity they could be able to clean substances with high resolution than other instruments


Methanotrophic bacteria consume methane as a carbon source.  Possibly being able to use these organisms to remove methane emissions from waster waters and toilets could improve smell of waste and reduce greenhouse gases

The Microbial Jungle….
October 1, 2010, 3:01 am
Filed under: Uncategorized

So, one phenomenon that I see a lot of research that interest me deals with microbial biofilms.  These assemblages of organisms, predominantly bacteria, are fascinating.  The reduced functions of these individuals are overcome thought organization of a community, smaller microenvironments, created though the anabolic/catabolic activities of other participants (Paerl and Pinckney 1996) .  This microbial facilitation can allow for presence of others which could not exist otherwise, for example, the existence of nitrogen fixing or reducing organisms living in an oxygenated environment. The coupling of these organism with another oxygen-consuming bacteria allows for the existence of a anoxic space within the film.

The mechanism at play here first seems have something to do with the separation of biochemical reactions withing different cells. Often times, each type of bacteria within the film is only capable of a single reaction to derive its energy source, but the biproduct of that reaction can facilitate the occurrance of others.   Compartmentalization is found in mutlitcelluar organims as well, but the microbes are able to work directly on the inorganic substrates of the environment, which presents them as a very useful subject for human manipulation and biomimetric innovation.

The study and understanding of these films, the organisms involved, the sequence of formation, and the stability of these communities, could yield many advantages in our manufacturing industries.  For example degredation of environmental pollutants (Macedo et al. 2007), or water treatment and reclaimation (Lydmark et al. 2007) are already areas where biofilms have potential to be used.  As we develop our abilities to engineer and maintain these microbial consortia many more uses will be discovered .  I find these aggregations fascinating and are akin to the forests of the tropics.  Like the forest, many prescious medicines and product lie within, if we can only take the time to look and see what is there.


Lydmark P, Almstrand R, Samuelsson K, Mattsson A, Sörensson F, Lindgren P.E.,  Hermansson M, (2007) Effects of environmental conditions on the nitrifying population dynamics in a pilot wastewater
treatment plant Environmental Microbiology (2007) 9(9), 2220–2233

Macedo A.J., Timmis K.N., Abraham W.R.(2007) Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination. Environmental Microbiology (2007) 9(8), 1890–1897

Paerl H.W., Pinckney J.L. (1996) A Mini-review of Microbial Consortia: Their Roles in Aquatic
Production and Biogeochemical Cycling. Microbial Ecology 31:225-247

Assignment 2 Cont’d….
September 24, 2010, 6:21 am
Filed under: Uncategorized

Part 3

When thinking of transport of materials, I think about the soil.  Much of the activity at this level we can’t observe, but this is where most of the action is happening.  Plants and fungus do a huge amount of work below ground, foraging through a complex matrix of organic and inorganic materials, fighting off pathogens, and competing with other organisms for much desired commodities such as nitrogen, phosphorus, and other necessary elements for growth.  They are at the interface between the biotic and abiotic environment, and often hold the majority of the food web on their shoulders…

But what makes them able to perform this job?  Both plants and fungi are distinctly different from animals, and interestingly enough, there are some commonalities between these two.  The design that makes one most fit for this job seems to include a few simple features, for instance, high surface-area to volume ratio, great absorptive capacity, and indeterminate growth.  Both the fine roots of plants, as well as the hyphal mats of the fungal mycelium have these features, even though these two organisms are evolutionarily, very distinct.   But, these features allow for continuous excavation of new territory, with no worry about the road home (indeterminant growth).  Also they have the best possible change or reaping the benefits of these efforts (amazing absorptive capacity, and high S-A:V).  This may be one of the reasons that fungi has been traditionally taught in sections of plant biology, even though the kingdoms are quite distinct.  Nevertheless, no one can deny that many of the organisms from both of these groups occupy niches in the environment that are intimately related to each other.

The most extreme case of this association has to be mycorrhizal associations that are made by the majority of plants and fungi.  These interactions connect these two organisms, creating a mutualism that has profound implications for ecosystem function.  For the plant, the smaller diameter of the fungal hyphae can penetrate into the soil at a much finer level and over a greater distance than the fine roots of one individual.  This provides increase access to water and nutrients (Liu et al. 1999).  For the Fungus, the carbon assimilated by the plant is a steady source of metabolites for this sojourning forager.

This interaction fits together so well, and is particularly interesting that the parts of organisms are so different and yet so similar in design.  Perhaps we can use some of these features, or perhaps these organisms for harvesting substances from the earth, just as the roots and fungus do….

Liu A., Hamel C., Hamilton R.I., Ma B.L., Smith D. L. (1999) Acquisition of Cu, Zn, Mn and Fe by mycorrhizal maize ( Zea mays L.) grown in soil at different P and micronutrient levels MYCORHIZZA 9:331-336

September 24, 2010, 5:45 am
Filed under: Uncategorized

Asssignment 2

Part 1

Here next to the water there is a small stand of trees, on the slope of a hill.  The canopy is high up and green, letting only small flecks of sunlight shine through.  A thin layer of leaf litter covers the ground and when kicked over reveals the fluffy white fungus, busy turning this material into small and small pieces.  Evidence of waterways, only brought to life with the summer rains, carves its channel all the way to the water.

Part 2


Organism: Oak tree (quercus) Strategy: (form) Oak seeds or acorns have a tough shell, which contains a single seed.  A mature Oak tree can be 40 ft tall, so this case for the seed can protect the seed from the drop to the canopy floor.  Also acorns are animal dispersed, and therefore need to survive transport and burial by organism such as squirrels or chipmunks.  In systems where oaks are present, they represent a major food source for many organisms.  For successful seedling establishment, they need to be able to survive seed predation, as well as the elements.

Organism:   Clover (trifolium) Strategy:  Leaves, this applies to any green plant but I already talked about trees.  Leaves contain photosynthetic apparatus to capture energy from the sun along with the biochemical pathways for fixing gaseous CO2 into sucrose.  As far as packaging, the ability to take the atomic components of the atmosphere and packages them into metabolites which can be used for growth and metabolism.

Water Purification

Organism: Fungus Strategy:  fungal hyphae penetrate the soil, foraging for organic matter to decompose.  These tubular strands (~5mm) form a dense mat that can exploit immense areas. This ingenious organism infiltrates the pore space and extract nitrogen, phosphorus, among other element from the soil solution.  Indeterminate growth, coupled with the small size of the hyphal strands gives it the ability to exploit resources that no others can rival.

Organism: Moss (Bryophytes) Strategy: spongy filtration.  Didn’t know what else to call this but these non-vascular plants, have always amazed me.  Their pioneer nature allows them to exploit and colonize habitats before all other.  But for purposes of water purification, these guys do some of the 1st steps in the process.  They seem to line these dried up streambeds, but when they are running these mosses serve to catch large particulate matter as the water flows though.  In this way they purify the water and also retaining some of the nutrients in the system.

Water availability

Organism:  Maple (acer) Strategy:  This becomes a little redundant for me, I feel as though I could pick the same organisms for all of these ecosystems functions.  But as per my previous blog, the action of deep rooting plants, penetrating to lower depths of the water table, couples with the tension force of evapotranspiration, create the process of hydraulic lift, pulling water from these depths to shallower parts of the soil, so that other can access these necessary commodity.

Organism: Fungus Strategy:  Again, the extensive network of the hyphal mycelium penetrates the soil.  The absorptive capacity of the hyphal particularly in mycorrhizal fungi works not only to find nutrients, but also functions in uptake of water from areas inaccessible to the plants root systems.

Transportation of materials

Organism:  Squirrel Strategy: Frugivory…the large teeth on these guys must play a role, as well as the claws for scaling trees, and the tail acts similar to a parachute in a fall.  All of these features allow these little guys to easily climb to the top of some of the tallest trees in the forest, harvest nuts, and then deliver them to sites for storage.  The process acts as a dispersal agent for the tree itself, when nuts are not eaten.  In any case, these little guys can move a lot of material from the tallest parts of the system, to the shortest.

Organism Penstemon (Penstemon Digitalis).  Strategy: this small flower does what all plants have the ability to do, transpire.  This elegant process is begins at the stomata of the leaf, where the H-bonding forces form a tension that is propagated back through the xylem cell, all the way back down to the roots, which pull up water from the soil.  This functions to carry water from the soil, and releases it back into the atmosphere where it will condense again and rain down on the land again.

Protection from biota

Organism: Wild Rosa.  Strategy:  Though this might by an invasive, they still provide a good example or protection from herbivores.  Having their stems lines with spines creates a barrier that makes them very hard to swallow, literally.  This must add to the strength of these plants to invade and do well in many habitats, because they are unlikely to be preyed upon by organisms looking for an easy meal

Organism: Snail Strategy:  The evolution of the shell was an amazing advantage to the mollusk.  With an extremely vulnerable body, which can fall prey to desiccation as well as table salt, possessing a harden shelter is beyond advantageous; it can be a lifesaver.  Once these organisms have crawled back into there shell they have are safe and sound.


Organism: Fungus Strategy:  The good old standby organism…through the process of uptake of nutrients, as well as the breakdown of decayed organic matter, these organism function as the ecosystem trash collectors and water treatment plants.  Their absorptive capacity allows them to remove many contaminants from soils components.  Fungus has can also break down synthetic products such as many petroleum base substances.

Organism: Bacteria Strategy:  Most of the time we think of cleaning in terms of removing bacteria, but the truth is, the diversity of organisms in this kingdom perform many essential functions in natural habitats.  Much in the same way that plant roots and fungus work, bacteria have the ability to take up soluble elements and remove them from water sources and sediments.  Bacterial immobilization of nitrate is a process, which can significant reduce the nitrogen load in some soils, and can be considered a form of cleaning.


Organism Fungus Strategy:  Here we go with the mushrooms again.  We can all see who my local champion is.  These guys are amazing in their hidden ecosystems services, as well as their beautiful elegance of form.  The hyphal structure works as a sponge, decomposing and absorbing is often the very definition of these organism ecological niche.

Organism Sedge roots Strategy:  I saw these grasses and decided to put them in here, but this applies to all plant roots.  Absorbing water as well as nutrient for growth and production of biomass connects this function to so many other ecosystem functions and services.  The small size and large surface area-to-volume ratio, makes these structures adequately equipped for exploitation of soils and uptake across cell membranes

Communication flows

Organism Birds Strategy:  I am no ornithologist, but out in this park I see orioles, terns, blackbirds, perhaps.  All I know is “cheep-cheep-cheep-cheep” is in the air.  These organisms define communications, and mastered it without the invention of the Blackberry mobile handset.  I don’t exactly know the process that gave them this ability; perhaps the chambered lung that aids in flying also contributes to being long winded.  It seems clear that they possess a very useful mechanism of communication.

Organism Deer:  Strategy:  Now I didn’t see any deer the day I was in the park, but I know they are there. Chances are, if they were at this site, they heard me coming, and moved on.  This brings me to my point…deer are unparalleled at there ability to sense their surroundings.  They seems to be aware at all times of the changes in the shadows, perhaps the wind, perhaps who knows

Feedback systems

Organism Oak/Beetle strategy:  I had to choose an interaction here and was inspired when I saw a small beetle eating a young oak sapling.  The dynamic between plant and herbivore is very interesting and is subject to shift in the natural environment.  Increases in atmospheric CO2 can increase growth of foliage, which can minimize the effect of losses due to herbivory.  On the hand, this can stimulate an increase in the beetle population, which can then effect the plant populations more intensely.

Organism Maple Strategy:  Through the process of evapotranspiration again, the magic of this function unfolds.  Water taken up from roots through this process is evaporated from the leaves, which goes into the gaseous atmosphere.  When it condenses, the water falls as rain, which is then taken up by the plant again.  In this way they plant acts directly in the biogeochemical cycling of freshwater.

Protection from abiotic factors (

Organism: Tree Canopy. Strategy:  The thick covering provided by the canopy tree shelters all under their shadow.  My taxonomic knowledge of east coast woody plants but I do see Oaks, Maples, Hickory, and others.   Outside of this tree stand, in an open field, you can feel wind blowing, the sun beating down, and during a rain, one could easily become soaked.  But within the canopy of these larger organism yields a much more gentle climate, providing shelter and protection for those that dwell within.

Organism: Snail Strategy:  For this had to look for a while, but almost be accident I almost stepped on this guy once I went closer to the waters edge.  This organism is interesting cause it provides its own protection.  Growing this shell helps protect them from predators as well as the elements, which is good because their skin will dry out quick.  Only problem for me is learning that the way the shell evolved, it turned the anus backwards, and that space where it puts it’s head in defense….well, lets just say I might rather be eaten….

Do Not Enter!
September 16, 2010, 9:10 pm
Filed under: Uncategorized

Walking by a junk yard I see one of the best deterrents….barbed or razor wire.  This invention, simple as it may be, lets all know that easy access to this area is not to be had. The origins of this were most likely inspired by the barbs and thorns of plant, which use these mechanical defenses to ward off potential grazers.

But at the cross roads between biological emmulation and biological utilization I remember a course from my undergrad.  In a course on greenhouse and nursery production, we went on field trips to see the industry.  At one citrus farm they originally tried to use this variety of orange as a root stock, but it was too aggressive and often choked the scion.  After that they sold it to office parks and other places for landscaping and security….so here the inspirations for the barbwire deterrents was actually used as the barbed wire…